Proteomics Report: DIA Benchmark Experiment

DE Analysis

Author

Andrea

Experiment

Yeast as background and USP2 proteins spiked in different concentration. This Experiment is designed for DIA benchmarking of different workflow using DIA-NN.

Import data

Reading DIA data from data/report.tsv using Precursor.Translated intensities from DIA-NN.

All the precursors with Q-value < 0.01 are used for the analysis.

Creating Q-Features object and run pre processing

The pre- processing steps are:

  • Filtering precursor with more than 3 samples with no missing intensities across all the samples
  • Select only proteotypic peptides
  • Select proteins with at least 3 peptides

Data Missing Analysis

Normalization

Raw intensities from DIA-NN are processed as follow:

  • Log 2 transformed
  • Normalized across all the samples using quantiles method
  • Summarization at protein level using **** function

PCA

DE Analysis

Using MSqRob2.

  GroupA   GroupB   GroupC   GroupD   GroupE 
15.13545 14.78455 14.88787 15.01882 15.01860 

QC plots

Group Comparison

Differential Expressed Proteins 

[1] “B” “A”

Differential Expressed Proteins 

[1] “D” “A”

Session Info

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_Belgium.utf8  LC_CTYPE=English_Belgium.utf8   
[3] LC_MONETARY=English_Belgium.utf8 LC_NUMERIC=C                    
[5] LC_TIME=English_Belgium.utf8    

time zone: Europe/Brussels
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] pheatmap_1.0.12             biomaRt_2.58.2             
 [3] gridExtra_2.3               ggVennDiagram_1.5.2        
 [5] hrbrthemes_0.8.7            factoextra_1.0.7           
 [7] MSnbase_2.28.1              ProtGenerics_1.34.0        
 [9] mzR_2.36.0                  Rcpp_1.0.12                
[11] DT_0.33                     plotly_4.10.4              
[13] here_1.0.1                  magrittr_2.0.3             
[15] lubridate_1.9.3             forcats_1.0.0              
[17] stringr_1.5.1               purrr_1.0.2                
[19] readr_2.1.5                 tidyr_1.3.1                
[21] tibble_3.2.1                ggplot2_3.5.0              
[23] tidyverse_2.0.0             dplyr_1.1.4                
[25] visdat_0.6.0                readxl_1.4.3               
[27] msqrob2_1.10.0              QFeatures_1.12.0           
[29] MultiAssayExperiment_1.28.0 SummarizedExperiment_1.32.0
[31] Biobase_2.62.0              GenomicRanges_1.54.1       
[33] GenomeInfoDb_1.38.8         IRanges_2.36.0             
[35] S4Vectors_0.40.2            BiocGenerics_0.48.1        
[37] MatrixGenerics_1.14.0       matrixStats_1.3.0          

loaded via a namespace (and not attached):
  [1] splines_4.3.3           later_1.3.2             bitops_1.0-7           
  [4] filelock_1.0.3          cellranger_1.1.0        preprocessCore_1.64.0  
  [7] XML_3.99-0.16.1         lifecycle_1.0.4         rstatix_0.7.2          
 [10] doParallel_1.0.17       rprojroot_2.0.4         lattice_0.22-6         
 [13] MASS_7.3-60.0.1         crosstalk_1.2.1         backports_1.4.1        
 [16] sass_0.4.9              limma_3.58.1            rmarkdown_2.26         
 [19] jquerylib_0.1.4         yaml_2.3.8              httpuv_1.6.15          
 [22] RColorBrewer_1.1-3      MsCoreUtils_1.14.1      DBI_1.2.2              
 [25] minqa_1.2.6             abind_1.4-5             zlibbioc_1.48.2        
 [28] AnnotationFilter_1.26.0 RCurl_1.98-1.14         rappdirs_0.3.3         
 [31] gdtools_0.3.7           GenomeInfoDbData_1.2.11 ggrepel_0.9.5          
 [34] crul_1.4.2              ncdf4_1.22              codetools_0.2-20       
 [37] DelayedArray_0.28.0     xml2_1.3.6              tidyselect_1.2.1       
 [40] farver_2.1.1            httpcode_0.3.0          lme4_1.1-35.3          
 [43] BiocFileCache_2.10.2    jsonlite_1.8.8          iterators_1.0.14       
 [46] systemfonts_1.0.6       foreach_1.5.2           tools_4.3.3            
 [49] progress_1.2.3          glue_1.7.0              BiocBaseUtils_1.4.0    
 [52] Rttf2pt1_1.3.12         SparseArray_1.2.4       xfun_0.43              
 [55] withr_3.0.0             BiocManager_1.30.22     fastmap_1.1.1          
 [58] boot_1.3-30             fansi_1.0.6             digest_0.6.35          
 [61] timechange_0.3.0        R6_2.5.1                mime_0.12              
 [64] colorspace_2.1-0        RSQLite_2.3.6           utf8_1.2.4             
 [67] generics_0.1.3          fontLiberation_0.1.0    data.table_1.15.4      
 [70] prettyunits_1.2.0       httr_1.4.7              htmlwidgets_1.6.4      
 [73] S4Arrays_1.2.1          pkgconfig_2.0.3         gtable_0.3.4           
 [76] blob_1.2.4              impute_1.76.0           XVector_0.42.0         
 [79] htmltools_0.5.8.1       carData_3.0-5           fontBitstreamVera_0.1.1
 [82] MALDIquant_1.22.2       clue_0.3-65             scales_1.3.0           
 [85] png_0.1-8               knitr_1.46              tzdb_0.4.0             
 [88] nlme_3.1-164            curl_5.2.1              nloptr_2.0.3           
 [91] cachem_1.0.8            parallel_4.3.3          extrafont_0.19         
 [94] AnnotationDbi_1.64.1    mzID_1.40.0             vsn_3.70.0             
 [97] pillar_1.9.0            grid_4.3.3              vctrs_0.6.5            
[100] pcaMethods_1.94.0       ggpubr_0.6.0            promises_1.3.0         
[103] car_3.1-2               dbplyr_2.5.0            xtable_1.8-4           
[106] cluster_2.1.6           extrafontdb_1.0         evaluate_0.23          
[109] cli_3.6.2               compiler_4.3.3          rlang_1.1.3            
[112] crayon_1.5.2            ggsignif_0.6.4          labeling_0.4.3         
[115] affy_1.80.0             plyr_1.8.9              stringi_1.8.3          
[118] viridisLite_0.4.2       BiocParallel_1.36.0     munsell_0.5.1          
[121] Biostrings_2.70.3       lazyeval_0.2.2          fontquiver_0.2.1       
[124] Matrix_1.6-5            hms_1.1.3               bit64_4.0.5            
[127] gfonts_0.2.0            KEGGREST_1.42.0         statmod_1.5.0          
[130] shiny_1.8.1.1           broom_1.0.5             igraph_2.0.3           
[133] memoise_2.0.1           bslib_0.7.0             affyio_1.72.0          
[136] bit_4.0.5